1
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Kato A. Development of conjugation-mediated versatile site-specific single-copy luciferase fusion system. J GEN APPL MICROBIOL 2024; 69:318-326. [PMID: 37940551 DOI: 10.2323/jgam.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
There are a number of reporter systems that are useful for gene expression analysis in bacteria. However, at least in Salmonella, a versatile and simple luciferase reporter system that can be integrated precisely behind a promoter or gene of interest on a chromosome is not currently available. The luciferase operon luxCDABE from Photorhabdus luminescens has several advantages, including brightness, wide linear range, absence in most bacteria, stability at high temperature, and no substrate addition required for the assay. Here, a conjugation-mediated site-specific single-copy luciferase fusion system is developed. A reporter plasmid containing the conditional replication origin R6Kgγ, FRT-luxCDABE, and KmR marker was designed to be incorporated into the FRT site behind the promoter or gene of interest on the chromosome in cells expressing FLP. However, when this reporter plasmid was electroporated directly into such a S. enterica strain, no colonies appeared, likely due to the low transformation efficiency of this relatively large plasmid DNA. Meanwhile, the same reporter plasmid was successfully introduced and launched as an insert of an FRT-containing conjugative transfer plasmid from a mating E. coli strain to the same recipient S. enterica strain, as well as Citrobacter koseri. RcsB-dependent inducible luminescence from the constructed wzc-luxCDABE strains was confirmed. This system is feasible for detecting very low levels of transcription, even in Gram-negative bacterial species that are relatively difficult to genetically manipulate.
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Affiliation(s)
- Akinori Kato
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University
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2
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Zhao Q, Bertolli S, Park YJ, Tan Y, Cutler KJ, Srinivas P, Asfahl KL, Fonesca-García C, Gallagher LA, Li Y, Wang Y, Coleman-Derr D, DiMaio F, Zhang D, Peterson SB, Veesler D, Mougous JD. Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 2024; 629:165-173. [PMID: 38632398 PMCID: PMC11062931 DOI: 10.1038/s41586-024-07298-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive1. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species1,2. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-electron microscopy structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, which led us to name them umbrella particles. Streptomyces coelicolor encodes three umbrella particles with distinct toxin and lectin composition. Notably, supernatant containing these toxins specifically and potently inhibits the growth of select Streptomyces species from among a diverse collection of bacteria screened. For one target, Streptomyces griseus, inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative hyphal growth. Our data show that Streptomyces umbrella particles mediate competition among vegetative mycelia of related species, a function distinct from small-molecule antibiotics, which are produced at the onset of reproductive growth and act broadly3,4. Sequence analyses suggest that this role of umbrella particles extends beyond Streptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria.
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Affiliation(s)
- Qinqin Zhao
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Savannah Bertolli
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Yongjun Tan
- Department of Biology, St Louis University, St Louis, MO, USA
| | - Kevin J Cutler
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Pooja Srinivas
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kyle L Asfahl
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA
| | - Citlali Fonesca-García
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Larry A Gallagher
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaqiao Li
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Devin Coleman-Derr
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Dapeng Zhang
- Department of Biology, St Louis University, St Louis, MO, USA
- Program of Bioinformatic and Computational Biology, St Louis University, St Louis, MO, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - David Veesler
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA.
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3
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Jiang X, Ke X, Tian X, Chu J. An inducible CRISPRi circuit for tunable dynamic regulation of gene expression in Saccharopolyspora erythraea. Biotechnol Lett 2024; 46:161-172. [PMID: 38279045 DOI: 10.1007/s10529-023-03462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/14/2023] [Accepted: 12/17/2023] [Indexed: 01/28/2024]
Abstract
Actinomyces are gram-positive bacteria known for their valuable secondary metabolites. Redirecting metabolic flux towards desired products in actinomycetes requires precise and dynamic regulation of gene expression. In this study, we integrated the CRISPR interference (CRISPRi) system with a cumate-inducible promoter to develop an inducible gene downregulation method in Saccharopolyspora erythraea, a prominent erythromycin-producing actinobacterium. The functionality of the cumate-inducible promoter was validated using the gusA gene as a reporter, and the successful inducible expression of the dCas9 gene was confirmed. The developed inducible CRISPRi strategy was then employed to downregulate the expression of target genes rppA in the wild-type strain NRRL2338 and sucC in the high erythromycin-producing strain E3. Through dynamic control of sucC expression, a significant enhancement in erythromycin production was achieved in strain E3. This study demonstrated the effectiveness of an inducible gene downregulation approach using CRISPRi and a cumate-inducible promoter, providing valuable insights for optimizing natural product production in actinomyces.
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Affiliation(s)
- Xing Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xiang Ke
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
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4
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Maleckis M, Wibowo M, Gren T, Jarmusch SA, Sterndorff EB, Booth T, Henriksen NNSE, Whitford CM, Jiang X, Jørgensen TS, Ding L, Weber T. Biosynthesis of the Azoxy Compound Azodyrecin from Streptomyces mirabilis P8-A2. ACS Chem Biol 2024; 19:641-653. [PMID: 38340355 DOI: 10.1021/acschembio.3c00632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Azoxy compounds are a distinctive group of bioactive secondary metabolites characterized by a unique RN═N+(O-)R moiety. The azoxy moiety is present in various classes of metabolites that exhibit various biological activities. The enzymatic mechanisms underlying azoxy bond formation remain enigmatic. Azodyrecins are cytotoxic azoxy metabolites produced by Streptomyces mirabilis P8-A2. Here, we cloned and confirmed the putative azd biosynthetic gene cluster through CATCH cloning followed by expression and production of azodyrecins in two heterologous hosts, S. albidoflavus J1074 and S. coelicolor M1146, respectively. We explored the function of 14 enzymes in azodyrecin biosynthesis through gene knockout using CRISPR-Cas9 base editing in the native producer, S. mirabilis P8-A2. The key intermediates were analyzed in the mutants through MS/MS fragmentation studies, revealing azoxy bond formation via the conversion of hydrazine to an azo compound followed by further oxygenation. Enzymes involved in modifications of the precursor could be postulated based on their predicted function and the intermediates identified in the knockout strains. Moreover, the distribution of the azoxy biosynthetic gene clusters across Streptomyces spp. genomes is explored, highlighting the presence of these clusters in over 20% of the Streptomyces spp. genomes and revealing that azoxymycin and valanimycin are scarce, while azodyrecin and KA57A-like clusters are widely distributed across the phylogenetic tree.
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Affiliation(s)
- Matiss Maleckis
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Eva B Sterndorff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Thomas Booth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Nathalie N S E Henriksen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Christopher M Whitford
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Tue S Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Ling Ding
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
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5
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Beganovic S, Rückert-Reed C, Sucipto H, Shu W, Gläser L, Patschkowski T, Struck B, Kalinowski J, Luzhetskyy A, Wittmann C. Systems biology of industrial oxytetracycline production in Streptomyces rimosus: the secrets of a mutagenized hyperproducer. Microb Cell Fact 2023; 22:222. [PMID: 37898787 PMCID: PMC10612213 DOI: 10.1186/s12934-023-02215-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Oxytetracycline which is derived from Streptomyces rimosus, inhibits a wide range of bacteria and is industrially important. The underlying biosynthetic processes are complex and hinder rational engineering, so industrial manufacturing currently relies on classical mutants for production. While the biochemistry underlying oxytetracycline synthesis is known to involve polyketide synthase, hyperproducing strains of S. rimosus have not been extensively studied, limiting our knowledge on fundamental mechanisms that drive production. RESULTS In this study, a multiomics analysis of S. rimosus is performed and wild-type and hyperproducing strains are compared. Insights into the metabolic and regulatory networks driving oxytetracycline formation were obtained. The overproducer exhibited increased acetyl-CoA and malonyl CoA supply, upregulated oxytetracycline biosynthesis, reduced competing byproduct formation, and streamlined morphology. These features were used to synthesize bhimamycin, an antibiotic, and a novel microbial chassis strain was created. A cluster deletion derivative showed enhanced bhimamycin production. CONCLUSIONS This study suggests that the precursor supply should be globally increased to further increase the expression of the oxytetracycline cluster while maintaining the natural cluster sequence. The mutagenized hyperproducer S. rimosus HP126 exhibited numerous mutations, including large genomic rearrangements, due to natural genetic instability, and single nucleotide changes. More complex mutations were found than those typically observed in mutagenized bacteria, impacting gene expression, and complicating rational engineering. Overall, the approach revealed key traits influencing oxytetracycline production in S. rimosus, suggesting that similar studies for other antibiotics could uncover general mechanisms to improve production.
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Affiliation(s)
- Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Hilda Sucipto
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Ben Struck
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany. *
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6
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Gao WL, Fang JL, Zhu CY, Xu WF, Lyu ZY, Chan XA, Zhao QW, Li YQ. Identification and Characterization of a New Regulator, TagR, for Environmental Stress Resistance Based on the DNA Methylome of Streptomyces roseosporus. Microbiol Spectr 2023; 11:e0038023. [PMID: 37154757 PMCID: PMC10269677 DOI: 10.1128/spectrum.00380-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/10/2023] [Indexed: 05/10/2023] Open
Abstract
DNA methylation is a defense that microorganisms use against extreme environmental stress, and improving resistance against environmental stress is essential for industrial actinomycetes. However, research on strain optimization utilizing DNA methylation for breakthroughs is rare. Based on DNA methylome analysis and KEGG pathway assignment in Streptomyces roseosporus, we discovered an environmental stress resistance regulator, TagR. A series of in vivo and in vitro experiments identified TagR as a negative regulator, and it is the first reported regulator of the wall teichoic acid (WTA) ABC transport system. Further study showed that TagR had a positive self-regulatory loop and m4C methylation in the promoter improved its expression. The ΔtagR mutant exhibited better hyperosmotic resistance and higher decanoic acid tolerance than the wild type, which led to a 100% increase in the yield of daptomycin. Moreover, enhancing the expression of the WTA transporter resulted in better osmotic stress resistance in Streptomyces lividans TK24, indicating the potential for wide application of the TagR-WTA transporter regulatory pathway. This research confirmed the feasibility and effectiveness of mining regulators of environmental stress resistance based on the DNA methylome, characterized the mechanism of TagR, and improved the resistance and daptomycin yield of strains. Furthermore, this research provides a new perspective on the optimization of industrial actinomycetes. IMPORTANCE This study established a novel strategy for screening regulators of environmental stress resistance based on the DNA methylome and discovered a new regulator, TagR. The TagR-WTA transporter regulatory pathway improved the resistance and antibiotic yield of strains and has the potential for wide application. Our research provides a new perspective on the optimization and reconstruction of industrial actinomycetes.
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Affiliation(s)
- Wen-Li Gao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Jiao-Le Fang
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Chen-Yang Zhu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Wei-Feng Xu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Zhong-Yuan Lyu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Xin-Ai Chan
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
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7
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Deng L, Zhao Z, Liu L, Zhong Z, Xie W, Zhou F, Xu W, Zhang Y, Deng Z, Sun Y. Dissection of 3D chromosome organization in Streptomyces coelicolor A3(2) leads to biosynthetic gene cluster overexpression. Proc Natl Acad Sci U S A 2023; 120:e2222045120. [PMID: 36877856 PMCID: PMC10242723 DOI: 10.1073/pnas.2222045120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023] Open
Abstract
The soil-dwelling filamentous bacteria, Streptomyces, is widely known for its ability to produce numerous bioactive natural products. Despite many efforts toward their overproduction and reconstitution, our limited understanding of the relationship between the host's chromosome three dimension (3D) structure and the yield of the natural products escaped notice. Here, we report the 3D chromosome organization and its dynamics of the model strain, Streptomyces coelicolor, during the different growth phases. The chromosome undergoes a dramatic global structural change from primary to secondary metabolism, while some biosynthetic gene clusters (BGCs) form special local structures when highly expressed. Strikingly, transcription levels of endogenous genes are found to be highly correlated to the local chromosomal interaction frequency as defined by the value of the frequently interacting regions (FIREs). Following the criterion, an exogenous single reporter gene and even complex BGC can achieve a higher expression after being integrated into the chosen loci, which may represent a unique strategy to activate or enhance the production of natural products based on the local chromosomal 3D organization.
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Affiliation(s)
- Liang Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Zhihu Zhao
- Department of Protein Engineering, Beijing Institute of Biotechnology, Beijing100071, China
| | - Lin Liu
- Epigenetic Division, Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan430075, China
| | - Zhiyu Zhong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Wenxinyu Xie
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Fan Zhou
- Epigenetic Division, Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan430075, China
| | - Wei Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Yubo Zhang
- Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518120, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
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8
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Li Y, Guan H, Li J, Zhang J, Wang Y, Li J, Tan H. An intricate regulation of WblA controlling production of silent tylosin analogues and abolishment of expressible nikkomycin. SCIENCE CHINA. LIFE SCIENCES 2023; 66:612-625. [PMID: 36607495 DOI: 10.1007/s11427-022-2199-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/21/2022] [Indexed: 01/07/2023]
Abstract
Genome sequencing has revealed that actinomycetes possess the potential to produce many more secondary metabolites than previously thought. The existing challenge is to devise efficient methods to activate these silent biosynthetic gene clusters (BGCs). In Streptomyces ansochromogenes, disruption of wblA, a pleiotropic regulatory gene, activated the expression of cryptic tylosin analogues and abolished nikkomycin production simultaneously. Overexpressing pathway-specific regulatory genes tylR1 and tylR2 can also trigger the biosynthesis of silent tylosin analogues, in which TylR1 exerted its function via enhancing tylR2 expression. Bacterial one-hybrid system experiments unveiled that WblA directly inhibits the transcription of tylR1 and tylR2 to result in the silence of tylosin analogues BGC. Furthermore, WblA can activate the nikkomycin production through up-regulating the transcription of pleiotropic regulatory gene adpA. More interestingly, AdpA can activate sanG (an activator gene in nikkomycin BGC) but repress wblA. Our studies provide a valuable insight into the complex functions of pleiotropic regulators.
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Affiliation(s)
- Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hanye Guan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jingjing Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanyan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jine Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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9
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Liu M, Wang K, Wei J, Liu N, Niu G, Tan H, Huang Y. Comparative and Functional Analyses Reveal Conserved and Variable Regulatory Systems That Control Lasalocid Biosynthesis in Different Streptomyces Species. Microbiol Spectr 2023; 11:e0385222. [PMID: 36847561 PMCID: PMC10100954 DOI: 10.1128/spectrum.03852-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/31/2023] [Indexed: 03/01/2023] Open
Abstract
Lasalocid, a representative polyether ionophore, has been successfully applied in veterinary medicine and animal husbandry and also displays promising potential for cancer therapy. Nevertheless, the regulatory system governing lasalocid biosynthesis remains obscure. Here, we identified two conserved (lodR2 and lodR3) and one variable (lodR1, found only in Streptomyces sp. strain FXJ1.172) putative regulatory genes through a comparison of the lasalocid biosynthetic gene cluster (lod) from Streptomyces sp. FXJ1.172 with those (las and lsd) from Streptomyces lasalocidi. Gene disruption experiments demonstrated that both lodR1 and lodR3 positively regulate lasalocid biosynthesis in Streptomyces sp. FXJ1.172, while lodR2 plays a negative regulatory role. To unravel the regulatory mechanism, transcriptional analysis and electrophoretic mobility shift assays (EMSAs) along with footprinting experiments were performed. The results revealed that LodR1 and LodR2 could bind to the intergenic regions of lodR1-lodAB and lodR2-lodED, respectively, thereby repressing the transcription of the lodAB and lodED operons, respectively. The repression of lodAB-lodC by LodR1 likely boosts lasalocid biosynthesis. Furthermore, LodR2 and LodE constitute a repressor-activator system that senses changes in intracellular lasalocid concentrations and coordinates its biosynthesis. LodR3 could directly activate the transcription of key structural genes. Comparative and parallel functional analyses of the homologous genes in S. lasalocidi ATCC 31180T confirmed the conserved roles of lodR2, lodE, and lodR3 in controlling lasalocid biosynthesis. Intriguingly, the variable gene locus lodR1-lodC from Streptomyces sp. FXJ1.172 seems functionally conserved when introduced into S. lasalocidi ATCC 31180T. Overall, our findings demonstrate that lasalocid biosynthesis is tightly controlled by both conserved and variable regulators, providing valuable guidance for further improving lasalocid production. IMPORTANCE Compared to its elaborated biosynthetic pathway, the regulation of lasalocid biosynthesis remains obscure. Here, we characterize the roles of regulatory genes in lasalocid biosynthetic gene clusters of two distinct Streptomyces species and identify a conserved repressor-activator system, LodR2-LodE, which could sense changes in the concentration of lasalocid and coordinate its biosynthesis with self-resistance. Furthermore, in parallel, we verify that the regulatory system identified in a new Streptomyces isolate is valid in the industrial lasalocid producer and thus applicable for the construction of high-yield strains. These findings deepen our understanding of regulatory mechanisms involved in the production of polyether ionophores and provide novel clues for the rational design of industrial strains for scaled-up production.
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Affiliation(s)
- Minghao Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kairui Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junhong Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guoqing Niu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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10
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Shi Y, Zhang J, Ma Z, Zhang Y, Bechthold A, Yu X. Double-reporter-guided targeted activation of the oxytetracycline silent gene cluster in Streptomyces rimosus M527. Biotechnol Bioeng 2023; 120:1411-1422. [PMID: 36775891 DOI: 10.1002/bit.28347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
In Streptomyces rimosus M527, the oxytetracycline (OTC) biosynthetic gene cluster is not expressed under laboratory conditions. In this study a reported-guided mutant selection (RGMS) procedure was used to activate the cluster. The double-reporter plasmid pAGT was constructed in which gusA encoding a β-glucuronidase and tsr encoding a thiostrepton resistance methyltransferase were placed under the control of the native promoter of oxyA gene (PoxyA ). Plasmid pAGT was introduced and integrated into the chromosome of S. rimosus M527 by conjugation, yielding initial strain M527-pAGT. Subsequently, mutants of M527-pAGT were generated by using ribosome engineering technology. The mutants harboring activated OTC gene cluster were selected based on visual observation of GUS activity and thiostrepton resistance. Finally, mutant M527-pAGT-R7 was selected producing OTC in a concentration of 235.2 mg/L. In this mutant transcriptional levels of oxysr genes especial oxyAsr gene were increased compared to wild-type strain S. rimosus M527. The mutant M527-pAGT-R7 showed antagonistic activities against Gram-negative and Gram-positive strains. All data indicate that the OTC gene cluster was successfully activated using the RGMS method.
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Affiliation(s)
- Yue Shi
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, China
| | - Jinyao Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, China
| | - Yongyong Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, China
| | - Andreas Bechthold
- Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, China
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11
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Tseduliak VM, Dolia B, Ostash I, Lopatniuk M, Busche T, Ochi K, Kalinowski J, Luzhetskyy A, Fedorenko V, Ostash B. Mutations within gene XNR_2147 for TetR-like protein enhance lincomycin resistance and endogenous specialized metabolism of Streptomyces albus J1074. J Appl Genet 2023; 64:185-195. [PMID: 36417169 DOI: 10.1007/s13353-022-00738-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Streptomyces albus J1074 is one of the most popular heterologous expression platforms among streptomycetes. Identification of new genes and mutations that influence specialized metabolism in this species is therefore of great applied interest. Here, we describe S. albus KO-1304 that was isolated as a spontaneous lincomycin-resistant variant of double rpsLR94G rsmGR15SG40E mutant KO-1295. Besides altered antibiotic resistance profile, KO-1304 exhibited increased antibiotic activity as compared to its parental strains. KO-1304 genome sequencing revealed mutations within gene XNR_2147 encoding putative TetR-like protein. Gene XNR_2146 for efflux protein is the most likely target of repressing action of Xnr_2147. Our data agree with the scenario where lincomycin resistance phenotype of KO-1304 arose from inability of mutated Xnr_2147 protein to repress XNR_2146. Introduction of additional copy of XNR_2146 into wild type strain increased antibiotic activity of the latter, attesting to the practical value of transporter genes for strain improvement.
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Affiliation(s)
- Vasylyna-Marta Tseduliak
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Borys Dolia
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Maria Lopatniuk
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123, Saarbrucken, Germany
| | - Tobias Busche
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Kozo Ochi
- Department of Life Sciences, Hiroshima Institute of Technology, Saeki-Ku, Hiroshima, 731-5193, Japan
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123, Saarbrucken, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine.
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12
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Heterologous Expression Reveals Ancient Properties of Tei3—A VanS Ortholog from the Teicoplanin Producer Actinoplanes teichomyceticus. Int J Mol Sci 2022; 23:ijms232415713. [PMID: 36555354 PMCID: PMC9779433 DOI: 10.3390/ijms232415713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Glycopeptide antibiotics (GPAs) are among the most clinically successful antimicrobials. GPAs inhibit cell-wall biosynthesis in Gram-positive bacteria via binding to lipid II. Natural GPAs are produced by various actinobacteria. Being themselves Gram-positives, the GPA producers evolved sophisticated mechanisms of self-resistance to avoid suicide during antibiotic production. These self-resistance genes are considered the primary source of GPA resistance genes actually spreading among pathogenic enterococci and staphylococci. The GPA-resistance mechanism in Actinoplanes teichomyceticus—the producer of the last-resort-drug teicoplanin—has been intensively studied in recent years, posing relevant questions about the role of Tei3 sensor histidine kinase. In the current work, the molecular properties of Tei3 were investigated. The setup of a GPA-responsive assay system in the model Streptomyces coelicolor allowed us to demonstrate that Tei3 functions as a non-inducible kinase, conferring high levels of GPA resistance in A. teichomyceticus. The expression of different truncated versions of tei3 in S. coelicolor indicated that both the transmembrane helices of Tei3 are crucial for proper functioning. Finally, a hybrid gene was constructed, coding for a chimera protein combining the Tei3 sensor domain with the kinase domain of VanS, with the latter being the inducible Tei3 ortholog from S. coelicolor. Surprisingly, such a chimera did not respond to teicoplanin, but indeed to the related GPA A40926. Coupling these experimental results with a further in silico analysis, a novel scenario on GPA-resistance and biosynthetic genes co-evolution in A. teichomyceticus was hereby proposed.
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13
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Novakova R, Homerova D, Csolleiova D, Rezuchova B, Sevcikova B, Javorova R, Feckova L, Kormanec J. A stable vector for efficient production of heterologous proteins and secondary metabolites in streptomycetes. Appl Microbiol Biotechnol 2022; 106:7285-7299. [PMID: 36173451 DOI: 10.1007/s00253-022-12187-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 11/24/2022]
Abstract
The bacteria of the genus Streptomyces are important producers of a large number of biologically active natural products. Examination of their genomes has revealed great biosynthetic potential for the production of new products, but many of them are silent under laboratory conditions. One of the promising avenues for harnessing this biosynthetic potential is the refactoring and heterologous expression of relevant biosynthetic gene clusters (BGCs) in suitable optimized chassis strains. Although several Streptomyces strains have been used for this purpose, the efficacy is relatively low, and some BGCs have not been expressed. In this study, we optimized our long-term genetically studied Streptomyces lavendulae subsp. lavendulae CCM 3239 strain as a potential host for heterologous expression along with its stable large linear plasmid pSA3239 as a vector system. Two reporter genes, mCherry and gusA under the control of ermEp* promoter, were successfully integrated into pSA3239. The activity of GUS reporter was four-fold higher in pSA3239 than in a single site in S. lavendulae subsp. lavendulae CCM 3239 chromosome, consistent with a higher copy number of pSA3239 (4 copies per chromosome). In addition, the two Att/Int systems (based on PhiC31 and pSAM2) were able to integrate into the corresponding individual attB sites in the chromosome. The BGC for actinorhodin was successfully integrated into pSA3239. However, the resulting strain produced very low amounts of actinorhodin. Its level increased dramatically after integration of the actII-ORF4 gene for the positive regulator under the control of the kasOp* promoter into this strain using the PhiC31 phage integration system. KEY POINTS: • New Streptomyces chassis for heterologous expression of genes and BGCs • Optimized strategy for insertion of heterologous genes into linear plasmid pSA3239 • Efficient heterologous production of actinorhodin after induction of its regulator.
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Affiliation(s)
- Renata Novakova
- Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovak Republic
| | - Dagmar Homerova
- Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovak Republic
| | - Dominika Csolleiova
- Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovak Republic
| | - Bronislava Rezuchova
- Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovak Republic
| | - Beatrica Sevcikova
- Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovak Republic
| | - Rachel Javorova
- Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovak Republic
| | - Lubomira Feckova
- Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovak Republic
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovak Republic.
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14
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Liu X, Li J, Li Y, Li J, Sun H, Zheng J, Zhang J, Tan H. A visualization reporter system for characterizing antibiotic biosynthetic gene clusters expression with high-sensitivity. Commun Biol 2022; 5:901. [PMID: 36056143 PMCID: PMC9440138 DOI: 10.1038/s42003-022-03832-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/11/2022] [Indexed: 11/09/2022] Open
Abstract
The crisis of antibiotic resistance has become an impending global problem. Genome sequencing reveals that streptomycetes have the potential to produce many more bioactive compounds that may combat the emerging pathogens. The existing challenge is to devise sensitive reporter systems for mining valuable antibiotics. Here, we report a visualization reporter system based on Gram-negative bacterial acyl-homoserine lactone quorum-sensing (VRS-bAHL). AHL synthase gene (cviI) of Chromobacterium violaceum as reporter gene is expressed in Gram-positive Streptomyces to synthesize AHL, which is detected with CV026, an AHL deficient mutant of C. violaceum, via its violacein production upon AHL induction. Validation assays prove that VRS-bAHL can be widely used for characterizing gene expression in Streptomyces. With the guidance of VRS-bAHL, a novel oxazolomycin derivative is discovered to the best of our knowledge. The results demonstrate that VRS-bAHL is a powerful tool for advancing genetic regulation studies and discovering valuable active metabolites in microorganisms. A quorum sensing based visualization reporter system is presented for the characterization of promoters in Gram-positive bacteria, utilizing violacein production, especially for use in the identification of secondary metabolites.
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Affiliation(s)
- Xiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jine Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Junyue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huiying Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiazhen Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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15
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Kennedy A, Griffin G, Freemont PS, Polizzi KM, Moore SJ. A curcumin direct protein biosensor for cell‐free prototyping. ENGINEERING BIOLOGY 2022; 6:62-68. [PMID: 36969103 PMCID: PMC9996706 DOI: 10.1049/enb2.12024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
In synthetic biology, biosensors are routinely coupled with a gene expression system for detecting small molecules and physical signals. We reveal a fluorescent complex, based on the interaction of an Escherichia coli double bond reductase (EcCurA), as a detection unit with its substrate curcumin-we call this a direct protein (DiPro) biosensor. Using a cell-free synthetic biology approach, we use the EcCurA DiPro biosensor to fine tune 10 reaction parameters (cofactor, substrate, and enzyme levels) for cell-free curcumin biosynthesis, assisted through acoustic liquid handling robotics. Overall, we increase EcCurA-curcumin DiPro fluorescence within cell-free reactions by 78-fold. This finding adds to the growing family of protein-ligand complexes that are naturally fluorescent and potentially exploitable for a range of applications, including medical imaging to engineering high-value chemicals.
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Affiliation(s)
- Agata Kennedy
- School of Biosciences University of Kent Canterbury UK
| | - Guy Griffin
- School of Biosciences University of Kent Canterbury UK
| | - Paul S. Freemont
- Centre for Synthetic Biology and Innovation South Kensington Campus London UK
- Department of Medicine South Kensington Campus London UK
- Department of Infectious Disease Section of Structural and Synthetic Biology Imperial College London London UK
- Sir Alexander Fleming Building South Kensington Campus London UK
- UK Dementia Research Institute Care Research and Technology Centre Imperial College London Hammersmith Campus London UK
| | - Karen M. Polizzi
- Centre for Synthetic Biology and Innovation South Kensington Campus London UK
- Department of Life Sciences Imperial College London South Kensington Campus London UK
- Department of Chemical Engineering Imperial College London South Kensington Campus London UK
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16
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Simple and reliable in situ CRISPR-Cas9 nuclease visualization tool is ensuring efficient editing in Streptomyces species. METHODS IN MICROBIOLOGY 2022; 200:106545. [DOI: 10.1016/j.mimet.2022.106545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/23/2022]
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17
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Surette MD, Waglechner N, Koteva K, Wright GD. HelR is a helicase-like protein that protects RNA polymerase from rifamycin antibiotics. Mol Cell 2022; 82:3151-3165.e9. [PMID: 35907401 DOI: 10.1016/j.molcel.2022.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 03/15/2022] [Accepted: 06/12/2022] [Indexed: 10/16/2022]
Abstract
Rifamycin antibiotics such as rifampin are potent inhibitors of prokaryotic RNA polymerase (RNAP) used to treat tuberculosis and other bacterial infections. Although resistance arises in the clinic principally through mutations in RNAP, many bacteria possess highly specific enzyme-mediated resistance mechanisms that modify and inactivate rifamycins. The expression of these enzymes is controlled by a 19-bp cis-acting rifamycin-associated element (RAE). Guided by the presence of RAE sequences, we identify a helicase-like protein, HelR, in Streptomyces venezuelae that confers broad-spectrum rifamycin resistance. We show that HelR also promotes tolerance to rifamycins, enabling bacterial evasion of the toxic properties of these antibiotics. HelR forms a complex with RNAP and rescues transcription inhibition by displacing rifamycins from RNAP, thereby providing resistance by target protection . Furthermore, HelRs are broadly distributed in Actinobacteria, including several opportunistic Mycobacterial pathogens, offering yet another challenge for developing new rifamycin antibiotics.
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Affiliation(s)
- Matthew D Surette
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Nicholas Waglechner
- Toronto Invasive Bacterial Diseases Network, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Kalinka Koteva
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Gerard D Wright
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.
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18
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Liu Y, Wang K, Pan L, Chen X. Improved Production of ε-Poly-L-Lysine in Streptomyces albulus Using Genome Shuffling and Its High-Yield Mechanism Analysis. Front Microbiol 2022; 13:923526. [PMID: 35711770 PMCID: PMC9195005 DOI: 10.3389/fmicb.2022.923526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022] Open
Abstract
ε-Poly-L-lysine (ε-PL), a natural food preservative, has recently gained interest and mainly produced by Streptomyces albulus. Lacking of efficient breeding methods limit ε-PL production improving, knockout byproducts and increase of main product flux strategies as a logical solution to increase yield. However, removing byproduct formation and improving main product synthesis has seen limited success due to the genetic background of ε-PL producing organism is not clear. To overcome this limitation, random mutagenesis continues to be the best way towards improving strains for ε-PL production. Recent advances in Illumina sequencing opened new avenues to understand improved strains. In this work, we used genome shuffling on strains obtained by ribosome engineering to generate a better ε-PL producing strain. The mutant strain SG-86 produced 144.7% more ε-PL than the parent strain M-Z18. Except that SG-86 displayed obvious differences in morphology and ATP compared to parent strain M-Z18. Using Illumina sequencing, we mapped the genomic changes leading to the improved phenotype. Sequencing two strains showed that the genome of the mutant strain was about 2.1 M less than that of the parent strain, including a large number of metabolic pathways, secondary metabolic gene clusters, and gene deletions. In addition, there are many SNPs (single nucleotide polymorphisms) and InDels (insertions and deletions) in the mutant strain. Based on the results of data analysis, a mechanism of ε-PL overproduction in S. albulus SG-86 was preliminarily proposed. This study is of great significance for improving the fermentation performance and providing theoretical guidance for the metabolic engineering construction of ε-PL producing strains.
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Affiliation(s)
- Yongjuan Liu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Shandong Energy Institute, Qingdao, China.,Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Kaifang Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Long Pan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Xusheng Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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19
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ClpP inhibitors are produced by a widespread family of bacterial gene clusters. Nat Microbiol 2022; 7:451-462. [PMID: 35246663 DOI: 10.1038/s41564-022-01073-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/31/2022] [Indexed: 11/08/2022]
Abstract
The caseinolytic protease (ClpP) is part of a highly conserved proteolytic complex whose disruption can lead to antibacterial activity but for which few specific inhibitors have been discovered. Specialized metabolites produced by bacteria have been shaped by evolution for specific functions, making them a potential source of selective ClpP inhibitors. Here, we describe a target-directed genome mining strategy for discovering ClpP-interacting compounds by searching for biosynthetic gene clusters that contain duplicated copies of ClpP as putative antibiotic resistance genes. We identify a widespread family of ClpP-associated clusters that are known to produce pyrrolizidine alkaloids but whose connection to ClpP has never been made. We show that previously characterized molecules do not affect ClpP function but are shunt metabolites derived from the genuine product of these gene clusters, a reactive covalent ClpP inhibitor. Focusing on one such cryptic gene cluster from Streptomyces cattleya, we identify the relevant inhibitor, which we name clipibicyclene, and show that it potently and selectively inactivates ClpP. Finally, we solve the crystal structure of clipibicyclene-modified Escherichia coli ClpP. Clipibicyclene's discovery reveals the authentic function of a family of natural products whose specificity for ClpP and abundance in nature illuminate the role of eco-evolutionary forces during bacterial competition.
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20
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He W, Wang W, Ma J, Zheng G, Zimin AA, Jiang W, Tian J, Lu Y. Crossregulation of rapamycin and elaiophylin biosynthesis by RapH in Streptomyces rapamycinicus. Appl Microbiol Biotechnol 2022; 106:2147-2159. [PMID: 35218390 DOI: 10.1007/s00253-022-11847-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 11/26/2022]
Abstract
Rapamycin is an important macrocyclic antibiotic produced by Streptomyces rapamycinicus. In the rapamycin biosynthetic gene cluster (BGC), there are up to five regulatory genes, which have been shown to play important roles in the regulation of rapamycin biosynthesis. Here, we demonstrated that the rapamycin BGC-situated LAL family regulator RapH co-ordinately regulated the biosynthesis of both rapamycin and elaiophylin. We showed that rapH overexpression not only resulted in enhanced rapamycin production but also led to increased synthesis of another type I polyketide antibiotic, elaiophylin. Consistent with this, rapH deletion resulted in decreased production of both antibiotics. Through real-time RT-PCR combined with β-glucuronidase reporter assays, four target genes controlled by RapH, including rapL (encoding a lysine cyclodeaminase)/rapH in the rapamycin BGC and ela3 (encoding a LuxR family regulator)/ela9 (encoding a hypothetical protein) in the elaiophylin BGC, were identified. A relatively conserved signature sequence recognized by RapH, which comprises two 4-nt inverted repeats separated by 8-nt, 5'-GTT/AC-N8-GTAC-3', was defined. Taken together, our findings demonstrated that RapH was involved in co-ordinated regulation of two disparate BGCs specifying two unrelated antibiotics, rapamycin and elaiophylin. These results further expand our knowledge of the regulation of antibiotic biosynthesis in S. rapamycinicus. KEY POINTS: • The cluster-situated regulator RapH controlled the synthesis of two antibiotics. • Four promoter regions recognized by RapH were identified. • A 16-nt signature DNA sequence essential for RapH regulation was defined.
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Affiliation(s)
- Wenyan He
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Wenfang Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jiaxiang Ma
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Guosong Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Andrei A Zimin
- G.K. Scriabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jinzhong Tian
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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21
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Melnyk S, Stepanyshyn A, Yushchuk O, Mandler M, Ostash I, Koshla O, Fedorenko V, Kahne D, Ostash B. Genetic approaches to improve clorobiocin production in Streptomyces roseochromogenes NRRL 3504. Appl Microbiol Biotechnol 2022; 106:1543-1556. [PMID: 35147743 PMCID: PMC9528727 DOI: 10.1007/s00253-022-11814-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 01/15/2023]
Abstract
Streptomyces roseochromogenes NRRL 3504 is best known as a producer of clorobiocin, a DNA replication inhibitor from the aminocoumarin family of antibiotics. This natural product currently draws attention as a promising adjuvant for co-application with other antibiotics against Gram-negative multidrug-resistant pathogens. Herein, we expand the genetic toolkit for NRRL 3504 by showing that a set of integrative and replicative vectors, not tested previously for this strain, could be conjugally transferred at high frequency from Escherichia coli to NRRL 3504. Using this approach, we leverage a cumate-inducible expression of cluster-situated regulatory gene novG to increase clorobiocin titers by 30-fold (up to approximately 200 mg/L). To our best knowledge, this is the highest level of clorobiocin production reported so far. Our findings set a working ground for further improvement of clorobiocin production as well as for the application of genetic methods to illuminate the cryptic secondary metabolome of NRRL 3504. Key Points • Efficient system for conjugative transfer of plasmids into NRRL 3504 was developed. • Expression of regulatory genes in NRRL 3504 led to increase in clorobiocin titer. • Secondary metabolome of NRRL 3504 becomes an accessible target for genetic manipulations using the expanded vector set and improved intergeneric conjugation protocol.
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Affiliation(s)
- Sofia Melnyk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Rm. 102, Lviv, 79005, Ukraine
| | - Anastasia Stepanyshyn
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Rm. 102, Lviv, 79005, Ukraine
| | - Oleksandr Yushchuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Rm. 102, Lviv, 79005, Ukraine
| | - Michael Mandler
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Rm. 102, Lviv, 79005, Ukraine
| | - Oksana Koshla
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Rm. 102, Lviv, 79005, Ukraine
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Rm. 102, Lviv, 79005, Ukraine
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Rm. 102, Lviv, 79005, Ukraine.
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22
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Zhao M, Wang M, Wang S, Xiong L, Gao B, Liu M, Tao X, Wang FQ, Wei D. A Self-Sustained System Spanning the Primary and Secondary Metabolism Stages to Boost the Productivity of Streptomyces. ACS Synth Biol 2022; 11:353-365. [PMID: 34951314 DOI: 10.1021/acssynbio.1c00473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Streptomyces species possess strong secondary metabolism, the switches of which from the primary metabolism are complex and thus a challenge to holistically optimize their productivities. To avoid the complex switches and to reduce the limitations of different metabolic stages on the synthesis of metabolites, we designed a Streptomyces self-sustained system (StSS) that contains two functional modules, the primary metabolism module (PM) and the secondary metabolism module (SM). The PM includes endogenous housekeeping sigma factor σhrdB and σhrdB-dependent promoters, which are used to express target genes in the primary metabolism phase. SM consists of the expression cassette of σhrdB under the control of a secondary metabolism promoter, which maintains continuous activity of the σhrdB-dependent promoters in the secondary metabolism phase. As a proof-of-principle, the StSS was used to boost the production of some non-toxic metabolites, including indigoidine, undecylprodigiosin (UDP), ergothioneine, and avermectin, in Streptomyces. All these metabolites can undergo a continuous production process spanning the primary and secondary metabolism stages instead of being limited to a specific stage. Scale-up of UDP fermentation in a 4 L fermentor indicated that the StSS is a stable and robust system, the titer of which was enhanced to 1.1 g/L, the highest at present. This study demonstrated that the StSS is a simple but powerful strategy to rationally engineer Streptomyces cell factories for the efficient production of non-toxic metabolites via reconstructing the relationships between primary and secondary metabolism.
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Affiliation(s)
- Ming Zhao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingrui Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Shuiling Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Liangbin Xiong
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Min Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xinyi Tao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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23
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Makitrynskyy R, Tsypik O, Bechthold A. Genetic Engineering of Streptomyces ghanaensis ATCC14672 for Improved Production of Moenomycins. Microorganisms 2021; 10:microorganisms10010030. [PMID: 35056478 PMCID: PMC8778134 DOI: 10.3390/microorganisms10010030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 01/11/2023] Open
Abstract
Streptomycetes are soil-dwelling multicellular microorganisms famous for their unprecedented ability to synthesize numerous bioactive natural products (NPs). In addition to their rich arsenal of secondary metabolites, Streptomyces are characterized by complex morphological differentiation. Mostly, industrial production of NPs is done by submerged fermentation, where streptomycetes grow as a vegetative mycelium forming pellets. Often, suboptimal growth peculiarities are the major bottleneck for industrial exploitation. In this work, we employed genetic engineering approaches to improve the production of moenomycins (Mm) in Streptomyces ghanaensis, the only known natural direct inhibitors of bacterial peptidoglycan glycosyltransferses. We showed that in vivo elimination of binding sites for the pleiotropic regulator AdpA in the oriC region strongly influences growth and positively correlates with Mm accumulation. Additionally, a marker- and “scar”-less deletion of moeH5, encoding an amidotransferase from the Mm gene cluster, significantly narrows down the Mm production spectrum. Strikingly, antibiotic titers were strongly enhanced by the elimination of the pleiotropic regulatory gene wblA, involved in the late steps of morphogenesis. Altogether, we generated Mm overproducers with optimized growth parameters, which are useful for further genome engineering and chemoenzymatic generation of novel Mm derivatives. Analogously, such a scheme can be applied to other Streptomyces spp.
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24
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Kim Y, Roe JH, Park JH, Cho YJ, Lee KL. Regulation of iron homeostasis by peroxide-sensitive CatR, a Fur-family regulator in Streptomyces coelicolor. J Microbiol 2021; 59:1083-1091. [PMID: 34865197 DOI: 10.1007/s12275-021-1457-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/08/2021] [Accepted: 10/20/2021] [Indexed: 11/30/2022]
Abstract
CatR, a peroxide-sensing transcriptional repressor of Fur family, can de-repress the transcription of the catA gene encoding catalase upon peroxide stress in Streptomyces coelicolor. Since CatR-regulated genes other than catA and its own gene catR have not been identified in detail, the understanding of the role of CatR regulon is very limited. In this study, we performed transcriptomic analysis to identify genes influenced by both ΔcatR mutation and hydrogen peroxide treatment. Through ChIP-qPCR and other analyses, a new consensus sequence was found in CatR-responsive promoter region of catR gene and catA operon for direct regulation. In addition, vtlA (SCO2027) and SCO4983 were identified as new members of the CatR regulon. Expression levels of iron uptake genes were reduced by hydrogen peroxide and a DmdR1 binding sequence was identified in promoters of these genes. The increase in free iron by hydrogen peroxide was thought to suppress the iron import system by DmdR1. A putative exporter protein VtlA regulated by CatR appeared to reduce intracellular iron to prevent oxidative stress. The name vtlA (VIT1-like transporter) was proposed for iron homeostasis related gene SCO2027.
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Affiliation(s)
- Yeonbum Kim
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jung-Hye Roe
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joo-Hong Park
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yong-Joon Cho
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea. .,The Research Institute of Basic Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Kang-Lok Lee
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 52828, Republic of Korea.
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25
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Screening and engineering of high-activity promoter elements through transcriptomics and red fluorescent protein visualization in Rhodobacter sphaeroides. Synth Syst Biotechnol 2021; 6:335-342. [PMID: 34738044 PMCID: PMC8531756 DOI: 10.1016/j.synbio.2021.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 12/03/2022] Open
Abstract
The versatile photosynthetic α-proteobacterium Rhodobacter sphaeroides, has recently been extensively engineered as a novel microbial cell factory (MCF) to produce pharmaceuticals, nutraceuticals, commodity chemicals and even hydrogen. However, there are no well-characterized high-activity promoters to modulate gene transcription during the engineering of R. sphaeroides. In this study, several native promoters from R. sphaeroides JDW-710 (JDW-710), an industrial strain producing high levels of co-enzyme Q10 (Q10) were selected on the basis of transcriptomic analysis. These candidate promoters were then characterized by using gusA as a reporter gene. Two native promoters, Prsp_7571 and Prsp_6124, showed 620% and 800% higher activity, respectively, than the tac promoter, which has previously been used for gene overexpression in R. sphaeroides. In addition, a Prsp_7571-derived synthetic promoter library with strengths ranging from 54% to 3200% of that of the tac promoter, was created on the basis of visualization of red fluorescent protein (RFP) expression in R. sphaeroides. Finally, as a demonstration, the synthetic pathway of Q10 was modulated by the selected promoter T334* in JDW-710; the Q10 yield in shake-flasks increased 28% and the production reached 226 mg/L. These well-characterized promoters should be highly useful in current synthetic biology platforms for refactoring the biosynthetic pathway in R. sphaeroides-derived MCFs.
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26
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Beck C, Gren T, Ortiz-López FJ, Jørgensen TS, Carretero-Molina D, Martín Serrano J, Tormo JR, Oves-Costales D, Kontou EE, Mohite OS, Mingyar E, Stegmann E, Genilloud O, Weber T. Activation and Identification of a Griseusin Cluster in Streptomyces sp. CA-256286 by Employing Transcriptional Regulators and Multi-Omics Methods. Molecules 2021; 26:6580. [PMID: 34770989 PMCID: PMC8588249 DOI: 10.3390/molecules26216580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
Streptomyces are well-known producers of a range of different secondary metabolites, including antibiotics and other bioactive compounds. Recently, it has been demonstrated that "silent" biosynthetic gene clusters (BGCs) can be activated by heterologously expressing transcriptional regulators from other BGCs. Here, we have activated a silent BGC in Streptomyces sp. CA-256286 by overexpression of a set of SARP family transcriptional regulators. The structure of the produced compound was elucidated by NMR and found to be an N-acetyl cysteine adduct of the pyranonaphtoquinone polyketide 3'-O-α-d-forosaminyl-(+)-griseusin A. Employing a combination of multi-omics and metabolic engineering techniques, we identified the responsible BGC. These methods include genome mining, proteomics and transcriptomics analyses, in combination with CRISPR induced gene inactivations and expression of the BGC in a heterologous host strain. This work demonstrates an easy-to-implement workflow of how silent BGCs can be activated, followed by the identification and characterization of the produced compound, the responsible BGC, and hints of its biosynthetic pathway.
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Affiliation(s)
- Charlotte Beck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Daniel Carretero-Molina
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Jesús Martín Serrano
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - José R. Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Eftychia E. Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Omkar S. Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Erik Mingyar
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (E.S.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Evi Stegmann
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (E.S.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
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27
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Lee JH, Lee EJ, Roe JH. uORF-mediated riboregulation controls transcription of whiB7/wblC antibiotic resistance gene. Mol Microbiol 2021; 117:179-192. [PMID: 34687261 DOI: 10.1111/mmi.14834] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/27/2022]
Abstract
WhiB7/WblC is a transcriptional factor of actinomycetes conferring intrinsic resistance to multiple translation-inhibitory antibiotics. It positively autoregulates its own transcription in response to the same antibiotics. The presence of a uORF and a potential Rho-independent transcription terminator in the 5' leader region has suggested a possibility that the whiB7/wblC gene is regulated via a uORF-mediated transcription attenuation. However, experimental evidence for the molecular mechanism to explain how antibiotic stress suppresses the attenuator, if any, and induces transcription of the whiB7/wblC gene has been lacking. Here we report that the 5' leader sequences of the whiB7/wblC genes in sub-clades of actinomycetes include conserved antiterminator RNA structures. We confirmed that the putative antiterminator in the whiB7/wblC leader sequences of both Streptomyces and Mycobacterium indeed suppresses Rho-independent transcription terminator and facilitates transcription readthrough, which is required for WhiB7/WblC-mediated antibiotic resistance. The antibiotic-mediated suppression of the attenuator can be recapitulated by amino acid starvation, indicating that translational inhibition of uORF by multiple signals is a key to induce whiB7/wblC expression. Our findings of a mechanism leading to intrinsic antibiotic resistance could provide an alternative to treat drug-resistant mycobacteria.
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Affiliation(s)
- Ju-Hyung Lee
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Jung-Hye Roe
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, Korea
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28
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Transcriptional regulation of congocidine (netropsin) biosynthesis and resistance. Appl Environ Microbiol 2021; 87:e0138021. [PMID: 34586912 DOI: 10.1128/aem.01380-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The production of specialized metabolites by Streptomyces bacteria is usually temporally regulated. This regulation is complex and frequently involves both global and pathway-specific mechanisms. Streptomyces ambofaciens ATCC23877 produces several specialized metabolites, including spiramycins, stambomycins, kinamycins and congocidine. The production of the first three molecules has been shown to be controlled by one or several cluster-situated transcriptional regulators. However, nothing is known regarding the regulation of congocidine biosynthesis. Congocidine (netropsin) belongs to the family of pyrrolamide metabolites, which also includes distamycin and anthelvencins. Most pyrrolamides bind into the minor groove of DNA, specifically in A/T-rich regions, which gives them numerous biological activities, such as antimicrobial and antitumoral activities. We previously reported the characterization of the pyrrolamide biosynthetic gene clusters of congocidine (cgc) in S. ambofaciens ATCC23877, distamycin (dst) in Streptomyces netropsis DSM40846 and anthelvencins (ant) in Streptomyces venezuelae ATCC14583. The three gene clusters contain a gene encoding a putative transcriptional regulator, cgc1, dst1 and ant1 respectively. Cgc1, Dst1 and Ant1 present a high percentage of amino acid sequence similarity. We demonstrate here that Cgc1, an atypical orphan response regulator, activates the transcription of all cgc genes in the stationary phase of S. ambofaciens growth. We also show that the cgc cluster is constituted of eight main transcriptional units. Finally, we show that congocidine induces the expression of the transcriptional regulator Cgc1 and of the operon containing the resistance genes (cgc20 and cgc21, coding for an ABC transporter), and propose a model for the transcriptional regulation of the cgc gene cluster. Importance Understanding the mechanisms of regulation of specialized metabolite production can have important implications both at the level of specialized metabolism study (expression of silent gene clusters) and the biotechnological level (increase of the production of a metabolite of interest). We report here a study on the regulation of the biosynthesis of a metabolite from the pyrrolamide family, congocidine. We show that congocidine biosynthesis and resistance is controlled by Cgc1, a cluster-situated regulator. As the gene clusters directing the biosynthesis of the pyrrolamides distamycin and anthelvencin encode a homolog of Cgc1, our findings may be relevant for the biosynthesis of other pyrrolamides. In addition, our results reveal a new type of feed-forward induction mechanism, in which congocidine induces its own biosynthesis through the induction of the transcription of cgc1.
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29
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Gren T, Whitford CM, Mohite OS, Jørgensen TS, Kontou EE, Nielsen JB, Lee SY, Weber T. Characterization and engineering of Streptomyces griseofuscus DSM 40191 as a potential host for heterologous expression of biosynthetic gene clusters. Sci Rep 2021; 11:18301. [PMID: 34526549 PMCID: PMC8443760 DOI: 10.1038/s41598-021-97571-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/19/2021] [Indexed: 12/20/2022] Open
Abstract
Streptomyces griseofuscus DSM 40191 is a fast growing Streptomyces strain that remains largely underexplored as a heterologous host. Here, we report the genome mining of S. griseofuscus, followed by the detailed exploration of its phenotype, including the production of native secondary metabolites and ability to utilise carbon, nitrogen, sulphur and phosphorus sources. Furthermore, several routes for genetic engineering of S. griseofuscus were explored, including use of GusA-based vectors, CRISPR-Cas9 and CRISPR-cBEST-mediated knockouts. Two out of the three native plasmids were cured using CRISPR-Cas9 technology, leading to the generation of strain S. griseofuscus DEL1. DEL1 was further modified by the full deletion of a pentamycin BGC and an unknown NRPS BGC, leading to the generation of strain DEL2, lacking approx. 500 kbp of the genome, which corresponds to a 5.19% genome reduction. DEL2 can be characterized by faster growth and inability to produce three main native metabolites: lankacidin, lankamycin, pentamycin and their derivatives. To test the ability of DEL2 to heterologously produce secondary metabolites, the actinorhodin BGC was used. We were able to observe a formation of a blue halo, indicating a potential production of actinorhodin by both DEL2 and a wild type.
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Affiliation(s)
- Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Christopher M Whitford
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Tue S Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Eftychia E Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Julie B Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, bygning 220, 2800, Kgs. Lyngby, Denmark.
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30
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Tran TT, Charles TC. Sequence polarity between the promoter and the adjacent gene modulates promoter activity. Plasmid 2021; 117:102598. [PMID: 34499918 DOI: 10.1016/j.plasmid.2021.102598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 11/26/2022]
Abstract
Promoter engineering has been employed as a strategy to enhance and optimize the production of bio-products. Availability of promoters with predictable activities is needed for downstream application. However, whether promoter activity remains the same in different gene contexts remains unknown. Six consecutive promoters that have previously been determined to have different activity levels were used to construct six different versions of plasmid backbone pTH1227, followed by inserted genes encoding two polymer-producing enzymes. In some cases, promoter activity in the presence of inserted genes did not correspond to the reported activity levels in a previous study. After removing the inserted genes, the activity of these promoters returned to their previously reported level. These changes were further confirmed to occur at the transcriptional level. Polymer production using our newly constructed plasmids showed polymer accumulation levels corresponding to the promoter activity reported in our study. Our study demonstrated the importance of re-assessing promoter activity levels with regard to gene context, which could influence promoter activity, leading to different outcomes in downstream applications.
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Affiliation(s)
- Tam T Tran
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada.
| | - Trevor C Charles
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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31
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Morris G, Gamage E, Travica N, Berk M, Jacka FN, O'Neil A, Puri BK, Carvalho AF, Bortolasci CC, Walder K, Marx W. Polyphenols as adjunctive treatments in psychiatric and neurodegenerative disorders: Efficacy, mechanisms of action, and factors influencing inter-individual response. Free Radic Biol Med 2021; 172:101-122. [PMID: 34062263 DOI: 10.1016/j.freeradbiomed.2021.05.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/14/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023]
Abstract
The pathophysiology of psychiatric and neurodegenerative disorders is complex and multifactorial. Polyphenols possess a range of potentially beneficial mechanisms of action that relate to the implicated pathways in psychiatric and neurodegenerative disorders. The aim of this review is to highlight the emerging clinical trial and preclinical efficacy data regarding the role of polyphenols in mental and brain health, elucidate novel mechanisms of action including the gut microbiome and gene expression, and discuss the factors that may be responsible for the mixed clinical results; namely, the role of interindividual differences in treatment response and the potentially pro-oxidant effects of some polyphenols. Further clarification as part of larger, well conducted randomized controlled trials that incorporate precision medicine methods are required to inform clinical efficacy and optimal dosing regimens.
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Affiliation(s)
- Gerwyn Morris
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Elizabeth Gamage
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Nikolaj Travica
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Michael Berk
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Felice N Jacka
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Adrienne O'Neil
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | | | - Andre F Carvalho
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Chiara C Bortolasci
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Ken Walder
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Wolfgang Marx
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia.
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Kontou EE, Gren T, Ortiz-López FJ, Thomsen E, Oves-Costales D, Díaz C, de la Cruz M, Jiang X, Jørgensen TS, Blin K, Charusanti P, Reyes F, Genilloud O, Weber T. Discovery and Characterization of Epemicins A and B, New 30-Membered Macrolides from Kutzneria sp. CA-103260. ACS Chem Biol 2021; 16:1456-1468. [PMID: 34279911 DOI: 10.1021/acschembio.1c00318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Actinobacteria have been a rich source of novel, structurally complex natural products for many decades. Although the largest genus is Streptomyces, from which the majority of antibiotics in current and past clinical use were originally isolated, other less common genera also have the potential to produce a wealth of novel secondary metabolites. One example is the Kutzneria genus, which currently contains only five reported species. One of these species is Kutzneria albida DSM 43870T, which has 46 predicted biosynthetic gene clusters and is known to produce the macrolide antibiotic aculeximycin. Here, we report the isolation and structural characterization of two novel 30-membered glycosylated macrolides, epemicins A and B, that are structurally related to aculeximycin, from a rare Kutzneria sp. The absolute configuration for all chiral centers in the two compounds is proposed based on extensive 1D and 2D NMR studies and bioinformatics analysis of the gene cluster. Through heterologous expression and genetic inactivation, we have confirmed the link between the biosynthetic gene cluster and the new molecules. These findings show the potential of rare Actinobacteria to produce new, structurally diverse metabolites. Furthermore, the gene inactivation represents the first published report to genetically manipulate a representative of the Kutzneria genus.
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Affiliation(s)
- Eftychia Eva Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Emil Thomsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
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33
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Interplay between Nucleoid-Associated Proteins and Transcription Factors in Controlling Specialized Metabolism in Streptomyces. mBio 2021; 12:e0107721. [PMID: 34311581 PMCID: PMC8406272 DOI: 10.1128/mbio.01077-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Lsr2 is a small nucleoid-associated protein found throughout the actinobacteria. Lsr2 functions similarly to the well-studied H-NS, in that it preferentially binds AT-rich sequences and represses gene expression. In Streptomyces venezuelae, Lsr2 represses the expression of many specialized metabolic clusters, including the chloramphenicol antibiotic biosynthetic gene cluster, and deleting lsr2 leads to significant upregulation of chloramphenicol cluster expression. We show here that Lsr2 likely exerts its repressive effects on the chloramphenicol cluster by polymerizing along the chromosome and by bridging sites within and adjacent to the chloramphenicol cluster. CmlR is a known activator of the chloramphenicol cluster, but expression of its associated gene is not upregulated in an lsr2 mutant strain. We demonstrate that CmlR is essential for chloramphenicol production, and further reveal that CmlR functions to “countersilence” Lsr2’s repressive effects by recruiting RNA polymerase and enhancing transcription, with RNA polymerase effectively clearing bound Lsr2 from the chloramphenicol cluster DNA. Our results provide insight into the interplay between opposing regulatory proteins that govern antibiotic production in S. venezuelae, which could be exploited to maximize the production of bioactive natural products in other systems.
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34
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Mickoleit F, Rosenfeldt S, Toro-Nahuelpan M, Schaffer M, Schenk AS, Plitzko JM, Schüler D. High-Yield Production, Characterization, and Functionalization of Recombinant Magnetosomes in the Synthetic Bacterium Rhodospirillum rubrum "magneticum". Adv Biol (Weinh) 2021; 5:e2101017. [PMID: 34296829 DOI: 10.1002/adbi.202101017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/10/2021] [Indexed: 01/02/2023]
Abstract
Recently, the photosynthetic Rhodospirillum rubrum has been endowed with the ability of magnetosome biosynthesis by transfer and expression of biosynthetic gene clusters from the magnetotactic bacterium Magnetospirillum gryphiswaldense. However, the growth conditions for efficient magnetite biomineralization in the synthetic R. rubrum "magneticum", as well as the particles themselves (i.e., structure and composition), have so far not been fully characterized. In this study, different cultivation strategies, particularly the influence of temperature and light intensity, are systematically investigated to achieve optimal magnetosome biosynthesis. Reduced temperatures ≤16 °C and gradual increase in light intensities favor magnetite biomineralization at high rates, suggesting that magnetosome formation might utilize cellular processes, cofactors, and/or pathways that are linked to photosynthetic growth. Magnetosome yields of up to 13.6 mg magnetite per liter cell culture are obtained upon photoheterotrophic large-scale cultivation. Furthermore, it is shown that even more complex, i.e., oligomeric, catalytically active functional moieties like enzyme proteins can be efficiently expressed on the magnetosome surface, thereby enabling the in vivo functionalization by genetic engineering. In summary, it is demonstrated that the synthetic R. rubrum "magneticum" is a suitable host for high-yield magnetosome biosynthesis and the sustainable production of genetically engineered, bioconjugated magnetosomes.
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Affiliation(s)
- Frank Mickoleit
- Dept. Microbiology, University of Bayreuth, D-95447, Bayreuth, Germany
| | - Sabine Rosenfeldt
- Bavarian Polymer Institute (BPI)/Physical Chemistry 1, University of Bayreuth, D-95447, Bayreuth, Germany
| | - Mauricio Toro-Nahuelpan
- Dept. Microbiology, University of Bayreuth, D-95447, Bayreuth, Germany.,Dept. Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Miroslava Schaffer
- Dept. Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Anna S Schenk
- Bavarian Polymer Institute (BPI)/Physical Chemistry - Colloidal Systems, University of Bayreuth, D-95447, Bayreuth, Germany
| | - Jürgen M Plitzko
- Dept. Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Dirk Schüler
- Dept. Microbiology, University of Bayreuth, D-95447, Bayreuth, Germany
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35
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Gläser L, Kuhl M, Stegmüller J, Rückert C, Myronovskyi M, Kalinowski J, Luzhetskyy A, Wittmann C. Superior production of heavy pamamycin derivatives using a bkdR deletion mutant of Streptomyces albus J1074/R2. Microb Cell Fact 2021; 20:111. [PMID: 34082758 PMCID: PMC8176718 DOI: 10.1186/s12934-021-01602-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Background Pamamycins are macrodiolides of polyketide origin which form a family of differently large homologues with molecular weights between 579 and 663. They offer promising biological activity against pathogenic fungi and gram-positive bacteria. Admittedly, production titers are very low, and pamamycins are typically formed as crude mixture of mainly smaller derivatives, leaving larger derivatives rather unexplored so far. Therefore, strategies that enable a more efficient production of pamamycins and provide increased fractions of the rare large derivatives are highly desired. Here we took a systems biology approach, integrating transcription profiling by RNA sequencing and intracellular metabolite analysis, to enhance pamamycin production in the heterologous host S. albus J1074/R2. Results Supplemented with l-valine, the recombinant producer S. albus J1074/R2 achieved a threefold increased pamamycin titer of 3.5 mg L−1 and elevated fractions of larger derivatives: Pam 649 was strongly increased, and Pam 663 was newly formed. These beneficial effects were driven by increased availability of intracellular CoA thioesters, the building blocks for the polyketide, resulting from l-valine catabolism. Unfavorably, l-valine impaired growth of the strain, repressed genes of mannitol uptake and glycolysis, and suppressed pamamycin formation, despite the biosynthetic gene cluster was transcriptionally activated, restricting production to the post l-valine phase. A deletion mutant of the transcriptional regulator bkdR, controlling a branched-chain amino acid dehydrogenase complex, revealed decoupled pamamycin biosynthesis. The regulator mutant accumulated the polyketide independent of the nutrient status. Supplemented with l-valine, the novel strain enabled the biosynthesis of pamamycin mixtures with up to 55% of the heavy derivatives Pam 635, Pam 649, and Pam 663: almost 20-fold more than the wild type. Conclusions Our findings open the door to provide rare heavy pamamycins at markedly increased efficiency and facilitate studies to assess their specific biological activities and explore this important polyketide further. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01602-6.
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Affiliation(s)
- Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Maksym Myronovskyi
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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36
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Engineering the precursor pool to modulate the production of pamamycins in the heterologous host S. albus J1074. Metab Eng 2021; 67:11-18. [PMID: 34051369 DOI: 10.1016/j.ymben.2021.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 12/20/2022]
Abstract
Pamamycins, a group of polyketides originally discovered in Streptomyces alboniger, induce sporulation in Streptomyces and inhibit the growth of Gram-positive bacteria, Mycobacterium tuberculosis and fungi. The pamamycin biosynthetic gene cluster encodes 6 ketosynthases that utilize a variety of three-carbon to five-carbon CoA thioesters as starter and extender units. This promiscuity in production results in an up to 18 different derivatives during fermentation. For more-selective production and simplified purification, we aimed to modify the precursor supply to narrow the spectrum of the produced derivatives. Eight genes potentially responsible for the supply of two major precursors, 2-S-methylmalonyl-CoA and 2-S-ethylmalonyl-CoA, were identified using the NCBI Basic Local Alignment Search Tool (BLAST) against the genome of the heterologous host S. albus J1074. Knockout mutants of the identified genes were constructed and their impact on intracellular CoA ester concentrations and on the production of pamamycins was determined. The created mutants enabled us to conclusively identify the ethylmalonyl-CoA supplying routes and their impact on the production of pamamycin. Furthermore, we gained significant information on the origin of the methylmalonyl-CoA supply in Streptomyces albus.
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37
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Slemc L, Pikl Š, Petković H, Avbelj M. Molecular Biology Methods in Streptomyces rimosus, a Producer of Oxytetracycline. Methods Mol Biol 2021; 2296:303-330. [PMID: 33977456 DOI: 10.1007/978-1-0716-1358-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Streptomyces rimosus is used for production of the broad-spectrum antibiotic oxytetracycline (OTC). S. rimosus belongs to Actinomyces species, a large group of microorganisms that produce diverse set of natural metabolites of high importance in many aspects of our life. In this chapter, we describe specific molecular biology methods and a classical homologous recombination approach for targeted in-frame deletion of a target gene or entire operon in S. rimosus genome. The presented protocols will guide you through the design of experiment and construction of homology arms and their cloning into appropriate vectors, which are suitable for gene-engineering work with S. rimosus. Furthermore, two different protocols for S. rimosus transformation are described including detailed procedure for targeted gene replacement via double crossover recombination event. Gene deletion is confirmed by colony PCR, and colonies are further characterized by cultivation and metabolite analysis. As the final step, we present in trans complementation of the deleted gene, to confirm functionality of the engineering approach achieved by gene disruption. A number of methodological steps and protocols are optimized for S. rimosus strains including the use of the selected reporter genes. Protocols described in this chapter can be applied for studying function of any individual gene product in diverse OTC-producing Streptomyces rimosus strains.
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Affiliation(s)
- Lucija Slemc
- Chair of Biotechnology, Microbiology and Food Safety, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Špela Pikl
- Chair of Biotechnology, Microbiology and Food Safety, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Hrvoje Petković
- Chair of Biotechnology, Microbiology and Food Safety, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Martina Avbelj
- Chair of Biotechnology, Microbiology and Food Safety, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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38
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Gongerowska-Jac M, Szafran MJ, Jakimowicz D. Combining transposon mutagenesis and reporter genes to identify novel regulators of the topA promoter in Streptomyces. Microb Cell Fact 2021; 20:99. [PMID: 33985526 PMCID: PMC8120823 DOI: 10.1186/s12934-021-01590-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying the regulatory factors that control transcriptional activity is a major challenge of gene expression studies. Here, we describe the application of a novel approach for in vivo identification of regulatory proteins that may directly or indirectly control the transcription of a promoter of interest in Streptomyces. RESULTS A method based on the combination of Tn5 minitransposon-driven random mutagenesis and lux reporter genes was applied for the first time for the Streptomyces genus. As a proof of concept, we studied the topA supercoiling-sensitive promoter, whose activity is dependent on unknown regulatory factors. We found that the sco4804 gene product positively influences topA transcription in S. coelicolor, demonstrating SCO4804 as a novel player in the control of chromosome topology in these bacteria. CONCLUSIONS Our approach allows the identification of novel Streptomyces regulators that may be critical for the regulation of gene expression in these antibiotic-producing bacteria.
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39
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The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes. Essays Biochem 2021; 65:261-275. [PMID: 33956071 DOI: 10.1042/ebc20200132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/08/2023]
Abstract
Streptomycetes are producers of a wide range of specialized metabolites of great medicinal and industrial importance, such as antibiotics, antifungals, or pesticides. Having been the drivers of the golden age of antibiotics in the 1950s and 1960s, technological advancements over the last two decades have revealed that very little of their biosynthetic potential has been exploited so far. Given the great need for new antibiotics due to the emerging antimicrobial resistance crisis, as well as the urgent need for sustainable biobased production of complex molecules, there is a great renewed interest in exploring and engineering the biosynthetic potential of streptomycetes. Here, we describe the Design-Build-Test-Learn (DBTL) cycle for metabolic engineering experiments in streptomycetes and how it can be used for the discovery and production of novel specialized metabolites.
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40
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Moore SJ, Lai HE, Chee SM, Toh M, Coode S, Chengan K, Capel P, Corre C, de los Santos ELC, Freemont PS. A Streptomyces venezuelae Cell-Free Toolkit for Synthetic Biology. ACS Synth Biol 2021; 10:402-411. [PMID: 33497199 PMCID: PMC7901020 DOI: 10.1021/acssynbio.0c00581] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Prokaryotic
cell-free coupled transcription–translation
(TX-TL) systems are emerging as a powerful tool to examine natural
product biosynthetic pathways in a test tube. The key advantages of
this approach are the reduced experimental time scales and controlled
reaction conditions. To realize this potential, it is essential to
develop specialized cell-free systems in organisms enriched for biosynthetic
gene clusters. This requires strong protein production and well-characterized
synthetic biology tools. The Streptomyces genus is
a major source of natural products. To study enzymes and pathways
from Streptomyces, we originally developed a homologous Streptomyces cell-free system to provide a native protein
folding environment, a high G+C (%) tRNA pool, and an active background
metabolism. However, our initial yields were low (36 μg/mL)
and showed a high level of batch-to-batch variation. Here, we present
an updated high-yield and robust Streptomyces TX-TL
protocol, reaching up to yields of 266 μg/mL of expressed recombinant
protein. To complement this, we rapidly characterize a range of DNA
parts with different reporters, express high G+C (%) biosynthetic
genes, and demonstrate an initial proof of concept for combined transcription,
translation, and biosynthesis of Streptomyces metabolic
pathways in a single “one-pot” reaction.
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Affiliation(s)
- Simon J. Moore
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Hung-En Lai
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Soo-Mei Chee
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- The London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Ming Toh
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Seth Coode
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Kameshwari Chengan
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Patrick Capel
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Christophe Corre
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Emmanuel LC de los Santos
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Paul S. Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- The London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0N, U.K
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Pikl Š, Carrillo Rincón AF, Slemc L, Goranovič D, Avbelj M, Gjuračić K, Sucipto H, Stare K, Baebler Š, Šala M, Guo M, Luzhetskyy A, Petković H, Magdevska V. Multiple copies of the oxytetracycline gene cluster in selected Streptomyces rimosus strains can provide significantly increased titers. Microb Cell Fact 2021; 20:47. [PMID: 33596911 PMCID: PMC7890619 DOI: 10.1186/s12934-021-01522-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/19/2021] [Indexed: 11/23/2022] Open
Abstract
Background Natural products are a valuable source of biologically active compounds that have applications in medicine and agriculture. One disadvantage with natural products is the slow, time-consuming strain improvement regimes that are necessary to ensure sufficient quantities of target compounds for commercial production. Although great efforts have been invested in strain selection methods, many of these technologies have not been improved in decades, which might pose a serious threat to the economic and industrial viability of such important bioprocesses. Results In recent years, introduction of extra copies of an entire biosynthetic pathway that encodes a target product in a single microbial host has become a technically feasible approach. However, this often results in minor to moderate increases in target titers. Strain stability and process reproducibility are the other critical factors in the industrial setting. Industrial Streptomyces rimosus strains for production of oxytetracycline are one of the most economically efficient strains ever developed, and thus these represent a very good industrial case. To evaluate the applicability of amplification of an entire gene cluster in a single host strain, we developed and evaluated various gene tools to introduce multiple copies of the entire oxytetracycline gene cluster into three different Streptomyces rimosus strains: wild-type, and medium and high oxytetracycline-producing strains. We evaluated the production levels of these engineered S. rimosus strains with extra copies of the oxytetracycline gene cluster and their stability, and the oxytetracycline gene cluster expression profiles; we also identified the chromosomal integration sites. Conclusions This study shows that stable and reproducible increases in target secondary metabolite titers can be achieved in wild-type and in high oxytetracycline-producing strains, which always reflects the metabolic background of each independent S. rimosus strain. Although this approach is technically very demanding and requires systematic effort, when combined with modern strain selection methods, it might constitute a very valuable approach in industrial process development.
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Affiliation(s)
- Špela Pikl
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Lucija Slemc
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Martina Avbelj
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Hilda Sucipto
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany.,Helmholtz-Institut für Pharmazeutische Forschung Saarland, Saarbrücken, Germany
| | - Katja Stare
- National Institute of Biology, Večna pot 111, Ljubljana, Slovenia
| | - Špela Baebler
- National Institute of Biology, Večna pot 111, Ljubljana, Slovenia
| | - Martin Šala
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany.,Helmholtz-Institut für Pharmazeutische Forschung Saarland, Saarbrücken, Germany
| | - Hrvoje Petković
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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42
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Regulatory Control of Rishirilide(s) Biosynthesis in Streptomyces bottropensis. Microorganisms 2021; 9:microorganisms9020374. [PMID: 33673359 PMCID: PMC7917814 DOI: 10.3390/microorganisms9020374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/27/2022] Open
Abstract
Streptomycetes are well-known producers of numerous bioactive secondary metabolites widely used in medicine, agriculture, and veterinary. Usually, their genomes encode 20-30 clusters for the biosynthesis of natural products. Generally, the onset and production of these compounds are tightly coordinated at multiple regulatory levels, including cluster-situated transcriptional factors. Rishirilides are biologically active type II polyketides produced by Streptomyces bottropensis. The complex regulation of rishirilides biosynthesis includes the interplay of four regulatory proteins encoded by the rsl-gene cluster: three SARP family regulators (RslR1-R3) and one MarR-type transcriptional factor (RslR4). In this work, employing gene deletion and overexpression experiments we revealed RslR1-R3 to be positive regulators of the biosynthetic pathway. Additionally, transcriptional analysis indicated that rslR2 is regulated by RslR1 and RslR3. Furthermore, RslR3 directly activates the transcription of rslR2, which stems from binding of RslR3 to the rslR2 promoter. Genetic and biochemical analyses demonstrated that RslR4 represses the transcription of the MFS transporter rslT4 and of its own gene. Moreover, DNA-binding affinity of RslR4 is strictly controlled by specific interaction with rishirilides and some of their biosynthetic precursors. Altogether, our findings revealed the intricate regulatory network of teamworking cluster-situated regulators governing the biosynthesis of rishirilides and strain self-immunity.
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Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO, Cho BK. Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes. Nat Prod Rep 2021; 38:1330-1361. [PMID: 33393961 DOI: 10.1039/d0np00071j] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2010 to 2020 Over the last few decades, Streptomyces have been extensively investigated for their ability to produce diverse bioactive secondary metabolites. Recent advances in Streptomyces research have been largely supported by improvements in high-throughput technology 'omics'. From genomics, numerous secondary metabolite biosynthetic gene clusters were predicted, increasing their genomic potential for novel bioactive compound discovery. Additional omics, including transcriptomics, translatomics, interactomics, proteomics and metabolomics, have been applied to obtain a system-level understanding spanning entire bioprocesses of Streptomyces, revealing highly interconnected and multi-layered regulatory networks for secondary metabolism. The comprehensive understanding derived from this systematic information accelerates the rational engineering of Streptomyces to enhance secondary metabolite production, integrated with the exploitation of the highly efficient 'Design-Build-Test-Learn' cycle in synthetic biology. In this review, we describe the current status of omics applications in Streptomyces research to better understand the organism and exploit its genetic potential for higher production of valuable secondary metabolites and novel secondary metabolite discovery.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yeo Joon Yoon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA. and Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
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pSETT4, an Improved φC31-Based Integrative Vector System for Actinoplanes sp. SE50/110. Microbiol Resour Announc 2020; 9:9/39/e00596-20. [PMID: 32972929 PMCID: PMC7516140 DOI: 10.1128/mra.00596-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pSETT4 vector integrates into the Actinoplanes sp. SE50/110 chromosome via the bacteriophage φC31 integrase and allows cloning of a gene of interest by Golden Gate assembly (BsaI). T4 terminators surround the expression cassette to isolate the transcriptional unit and to prevent antisense transcription. The system can be used in other Actinomycetales by exchanging the promoter.
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Li Y, Zhang J, Zheng J, Guan H, Liu W, Tan H. Co-expression of a SARP Family Activator ChlF2 and a Type II Thioesterase ChlK Led to High Production of Chlorothricin in Streptomyces antibioticus DSM 40725. Front Bioeng Biotechnol 2020; 8:1013. [PMID: 32974326 PMCID: PMC7471628 DOI: 10.3389/fbioe.2020.01013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/03/2020] [Indexed: 11/20/2022] Open
Abstract
Chlorothricin (CHL), produced by Streptomyces antibioticus DSM 40725 (wild-type strain, WT), belongs to a growing family of spirotetronate antibiotics that have biological activities inhibiting pyruvate carboxylase and malate dehydrogenase. ChlF2, a cluster-situated SARP regulator, can activate the transcription of chlJ, chlC3, chlC6, chlE1, chlM, and chlL to control CHL biosynthesis. Co-expression of chlF2 and chlK encoding type II thioesterase in WT strain under the control of Pkan led to high production of chlorothricin by 840% in comparison with that of WT. Since the inhibitory activity of CHL against several Gram-positive bacteria is higher than des-CHL, combinatorial strategies were applied to promote the conversion of des-CHL to CHL. Over-expression of chlB4, encoding a halogenase, combining with the supplementation of sodium chloride led to further 41% increase of CHL production compared to that of F2OE, a chlF2 over-expression strain. These findings provide new insights into the fine-tuned regulation of spirotetronate family of antibiotics and the construction of high-yield engineered strains.
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Affiliation(s)
- Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiazhen Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hanye Guan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Li X, Chu J, Jensen PR. The Expression of NOX From Synthetic Promoters Reveals an Important Role of the Redox Status in Regulating Secondary Metabolism of Saccharopolyspora erythraea. Front Bioeng Biotechnol 2020; 8:818. [PMID: 32766231 PMCID: PMC7379104 DOI: 10.3389/fbioe.2020.00818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/26/2020] [Indexed: 12/17/2022] Open
Abstract
Redox cofactors play a pivotal role in primary cellular metabolism, whereas the clear link between redox status and secondary metabolism is still vague. In this study we investigated effects of redox perturbation on the production of erythromycin in Saccharopolyspora erythraea by expressing the water-forming NADH oxidase (NOX) from Streptococcus pneumonia at different levels with synthetic promoters. The expression of NOX reduced the intracellular [NADH]/[NAD+] ratio significantly in S. erythraea which resulted in an increased production of erythromycin by 19∼29% and this increment rose to 60% as more oxygen was supplied. In contrast, the lower redox ratio resulted in a decreased production of another secondary metabolite, the reddish pigment 7-O-rahmnosyl flaviolin. The metabolic shifts of secondary metabolism results in a higher NADH availability which compensates for its oxidization via NOX. The expression of the erythromycin biosynthesis gene cluster (BGC) in the NOX-expression strains was upregulated as the activity of diguanylate cyclase was inhibited moderately by NADH. This study also suggested that lower intracellular [NADH]/[NAD+] ratio benefits the biosynthesis of erythromycin by potentially affecting the biosynthesis of the secondary messenger, bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), which may stimulate the positive regulation of erythromycin BGC via BldD. The present work provides a basis for future cofactor manipulation in S. erythraea to improve the industrial production of erythromycin.
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Affiliation(s)
- Xiaobo Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Peter R Jensen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Cyclic di-GMP cyclase SSFG_02181 from Streptomyces ghanaensis ATCC14672 regulates antibiotic biosynthesis and morphological differentiation in streptomycetes. Sci Rep 2020; 10:12021. [PMID: 32694623 PMCID: PMC7374567 DOI: 10.1038/s41598-020-68856-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
Streptomycetes are filamentous bacteria famous for their ability to produce a vast majority of clinically important secondary metabolites. Both complex morphogenesis and onset of antibiotic biosynthesis are tightly linked in streptomycetes and require series of specific signals for initiation. Cyclic dimeric 3′–5′ guanosine monophosphate, c-di-GMP, one of the well-known bacterial second messengers, has been recently shown to govern morphogenesis and natural product synthesis in Streptomyces by altering the activity of the pleiotropic regulator BldD. Here we report a role of the heme-binding diguanylate cyclase SSFG_02181 from Streptomyces ghanaensis in the regulation of the peptidoglycan glycosyltransferase inhibitor moenomycin A biosynthesis. Deletion of ssfg_02181 reduced the moenomycin A accumulation and led to a precocious sporulation, while the overexpression of the gene blocked sporogenesis and remarkably improved antibiotic titer. We also demonstrate that BldD negatively controls the expression of ssfg_02181, which stems from direct binding of BldD to the ssfg_02181 promoter. Notably, the heterologous expression of ssfg_02181 in model Streptomyces spp. arrested morphological progression at aerial mycelium level and strongly altered the production of secondary metabolites. Altogether, our work underscores the significance of c-di-GMP-mediated signaling in natural product biosynthesis and pointed to extensively applicable approach to increase antibiotic production levels in streptomycetes.
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Edenhart S, Denneler M, Spohn M, Doskocil E, Kavšček M, Amon T, Kosec G, Smole J, Bardl B, Biermann M, Roth M, Wohlleben W, Stegmann E. Metabolic engineering of Amycolatopsis japonicum for optimized production of [S,S]-EDDS, a biodegradable chelator. Metab Eng 2020; 60:148-156. [PMID: 32302770 DOI: 10.1016/j.ymben.2020.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/23/2020] [Accepted: 04/06/2020] [Indexed: 11/16/2022]
Abstract
The actinomycete Amycolatopsis japonicum is the producer of the chelating compound [S,S]-ethylenediamine-disuccinc acid (EDDS). [S,S]-EDDS is an isomer of ethylenediamine-tetraacetic acid (EDTA), an economically important chelating compound that suffers from an extremely poor degradability. Frequent use of the persistent EDTA in various industrial and domestic applications has caused an accumulation of EDTA in soil as well as in aqueous environments. As a consequence, EDTA is the highest concentrated anthropogenic compound present in water reservoirs. The [S,S]-form of EDDS has chelating properties similar to EDTA, however, in contrast to EDTA it is readily biodegradable. In order to compete with the cost-effective chemical synthesis of EDTA, we aimed to optimize the biotechnological production of [S,S]-EDDS in A. japonicum by using metabolic engineering approaches. Firstly, we integrated several copies of the [S,S]-EDDS biosynthetic genes into the chromosome of A. japonicum and replaced the native zinc responsive promoter with the strong synthetic constitutive promoter SP44*. Secondly, we increased the supply of O-phospho-serine, the direct precursor of [S,S]-EDDS. The combination of these approaches together with the optimized fermentation process led to a significant improvement in [S,S]-EDDS up to 9.8 g/L with a production rate of 4.3 mg/h/g DCW.
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Affiliation(s)
- Simone Edenhart
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - Marius Denneler
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - Marius Spohn
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - Eva Doskocil
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - Martin Kavšček
- Acies Bio d.o.o., Tehnoloski Park 21, 1000, Ljubljana, Slovenia
| | - Tadeja Amon
- Acies Bio d.o.o., Tehnoloski Park 21, 1000, Ljubljana, Slovenia
| | - Gregor Kosec
- Acies Bio d.o.o., Tehnoloski Park 21, 1000, Ljubljana, Slovenia
| | - Jernej Smole
- Acies Bio d.o.o., Tehnoloski Park 21, 1000, Ljubljana, Slovenia
| | - Bettina Bardl
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Bio Pilot Plant, Beutenbergstr. 11A, 07745, Jena, Germany
| | - Michael Biermann
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Bio Pilot Plant, Beutenbergstr. 11A, 07745, Jena, Germany
| | - Martin Roth
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Bio Pilot Plant, Beutenbergstr. 11A, 07745, Jena, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Germany.
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Mickoleit F, Lanzloth C, Schüler D. A Versatile Toolkit for Controllable and Highly Selective Multifunctionalization of Bacterial Magnetic Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1906922. [PMID: 32187836 DOI: 10.1002/smll.201906922] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 05/18/2023]
Abstract
Their unique material characteristics, i.e. high crystallinity, strong magnetization, uniform shape and size, and the ability to engineer the enveloping membrane in vivo make bacterial magnetosomes highly interesting for many biomedical and biotechnological applications. In this study, a versatile toolkit is developed for the multifunctionalization of magnetic nanoparticles in the magnetotactic bacterium Magnetospirillum gryphiswaldense, and the use of several abundant magnetosome membrane proteins as anchors for functional moieties is explored. High-level magnetosome display of cargo proteins enables the generation of engineered nanoparticles with several genetically encoded functionalities, including a core-shell structure, magnetization, two different catalytic activities, fluorescence and the presence of a versatile connector that allows the incorporation into a hydrogel-based matrix by specific coupling reactions. The resulting reusable magnetic composite demonstrates the high potential of synthetic biology for the production of multifunctional nanomaterials, turning the magnetosome surface into a platform for specific versatile display of functional moieties.
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Affiliation(s)
- Frank Mickoleit
- Department of Microbiology, University of Bayreuth, Universitätsstraße 30, Bayreuth, D-95447, Germany
| | - Clarissa Lanzloth
- Department of Microbiology, University of Bayreuth, Universitätsstraße 30, Bayreuth, D-95447, Germany
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Universitätsstraße 30, Bayreuth, D-95447, Germany
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Song Z, Ma Z, Bechthold A, Yu X. Effects of addition of elicitors on rimocidin biosynthesis in Streptomyces rimosus M527. Appl Microbiol Biotechnol 2020; 104:4445-4455. [PMID: 32221690 DOI: 10.1007/s00253-020-10565-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 01/25/2023]
Abstract
The polyene macrolide rimocidin, produced by Streptomyces rimosus M527, is highly effective against a broad range of fungal plant pathogens, but at low yields. Elicitation is an effective method of stimulating the yield of bioactive secondary metabolites. In this study, the biomass and filtrate of a culture broth of Escherichia coli JM109, Bacillus subtilis WB600, Saccharomyces cerevisiae, and Fusarium oxysporum f. sp. cucumerinum were employed as elicitors to promote rimocidin production in S. rimosus M527. Adding culture broth and biomass of S. cerevisiae (A3) and F. oxysporum f. sp. cucumerinum (B4) resulted in an increase of rimocidin production by 51.2% and 68.3% respectively compared with the production under normal conditions in 5-l fermentor. In addition, quantitative RT-PCR analysis revealed that the transcriptions of ten genes (rimA to rimK) located in the gene cluster involved in rimocidin biosynthesis in A3 or B4 elicitation experimental group were all higher than those of a control group. Using a β-glucuronidase (GUS) reporter system, GUS enzyme activity assay, and Western blot analysis, we discovered that elicitation of A3 or B4 increased protein synthesis in S. rimosus M527. These results demonstrate that the addition of elicitors is a useful approach to improve rimocidin production.Key Points • An effective strategy for enhancing rimocidin production in S. rimosus M527 is demonstrated. • Overproduction of rimocidin is a result of higher expressed structural genes followed by an increase in protein synthesis.
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Affiliation(s)
- Zhangqing Song
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, People's Republic of China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, People's Republic of China.
| | - Andreas Bechthold
- Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, University of Freiburg, 79104, Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, People's Republic of China
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